LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-836-ge548c656ce)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
  using 1 OpenMP thread(s) per MPI task
variable	sname index adamantane_ionized

units 		electron
newton		on
boundary        f f f

atom_style	electron

read_data  	data.${sname}
read_data  	data.adamantane_ionized
Reading data file ...
  orthogonal box = (-50 -50 -50) to (50 50 50)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  101 atoms
  read_data CPU = 0.038 seconds

pair_style      eff/cut 100.0
pair_coeff 	* *

comm_modify	vel yes

compute		effTemp all temp/eff

thermo		1000
thermo_style	custom step pe temp etotal press
thermo_modify	temp effTemp

# Minimization
min_style       cg
dump            1 all xyz 500 ${sname}.min.xyz
dump            1 all xyz 500 adamantane_ionized.min.xyz
compute         1 all property/atom spin eradius erforce
dump            2 all custom 500 ${sname}.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
dump            2 all custom 500 adamantane_ionized.min.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
min_modify	line quadratic
minimize        0.0 1.0e-5 10000 100000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- EFF package: doi:10.1002/jcc.21637

@Article{Jaramillo-Botero11,
 author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
 title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
 journal = {J.~Comp.\ Chem.},
 year =    2011,
 volume =  32,
 number =  3,
 pages =   {497--512}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 102
  ghost atom cutoff = 102
  binsize = 51, bins = 2 2 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair eff/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.222 | 5.222 | 5.222 Mbytes
   Step         PotEng          Temp          TotEng         Press     
         0  -320.50186      0             -320.50186     -45590269     
       571  -324.30072      0             -324.30072      21193099     
Loop time of 2.61846 on 1 procs for 571 steps with 101 atoms

99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = linesearch alpha is zero
  Energy initial, next-to-last, final = 
     -320.501859657303   -324.30071870307   -324.30071870307
  Force two-norm initial, final = 2.8135352 2.2777398
  Force max component initial, final = 1.7194878 2.093044
  Final line search alpha, max atom move = 2.2781994e-09 4.7683716e-09
  Iterations, force evaluations = 571 5621

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 2.602      | 2.602      | 2.602      |   0.0 | 99.37
Neigh   | 2.5097e-05 | 2.5097e-05 | 2.5097e-05 |   0.0 |  0.00
Comm    | 0.00046417 | 0.00046417 | 0.00046417 |   0.0 |  0.02
Output  | 0.00029579 | 0.00029579 | 0.00029579 |   0.0 |  0.01
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.0157     |            |       |  0.60

Nlocal:            101 ave         101 max         101 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:           5050 ave        5050 max        5050 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 5050
Ave neighs/atom = 50
Neighbor list builds = 1
Dangerous builds = 0

undump		1
undump		2

#restart		timestep

# set velocities for nve
#velocity	all create 300.0 4928459 dist uniform

# NVE
timestep	0.0001

fix		1 all nve/eff
dump            1 all xyz 1000 ${sname}.nve.xyz
dump            1 all xyz 1000 adamantane_ionized.nve.xyz
dump            2 all custom 1000 ${sname}.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
dump            2 all custom 1000 adamantane_ionized.nve.lammpstrj id type x y z c_1[1] c_1[2] fx fy fz c_1[3]
#restart		1000 ${sname}.nve.restart1 ${sname}.nve.restart2

run		200000
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.097 | 4.097 | 4.097 Mbytes
   Step         PotEng          Temp          TotEng         Press     
       571  -324.30072      0             -324.30072      21193099     
      1000  -324.00833      75606.318     -315.02966      1.9184325e+08
      2000  -322.45879      62558.11      -315.02966      1.4564261e+08
      3000  -322.01495      58820.681     -315.02966      1.3051251e+08
      4000  -321.3178       52950.225     -315.02966      75989118     
      5000  -320.89488      49388.959     -315.02966      55413771     
      6000  -320.97564      50069.086     -315.02966      67105302     
      7000  -320.9772       50082.172     -315.02966      90728737     
      8000  -320.76927      48331.305     -315.02966      1.1054849e+08
      9000  -320.40821      45290.936     -315.02966      1.1325434e+08
     10000  -320.10216      42713.788     -315.02966      1.0766253e+08
     11000  -320.00263      41875.679     -315.02966      1.0831982e+08
     12000  -319.92006      41180.36      -315.02966      1.0888686e+08
     13000  -319.85913      40667.331     -315.02966      1.0763265e+08
     14000  -319.86056      40679.317     -315.02966      1.1159571e+08
     15000  -319.79071      40091.129     -315.02966      1.1261281e+08
     16000  -319.7393       39658.231     -315.02966      1.0983394e+08
     17000  -319.74963      39745.211     -315.02966      1.12573e+08  
     18000  -319.70347      39356.518     -315.02966      1.1249278e+08
     19000  -319.68924      39236.684     -315.02966      1.084432e+08 
     20000  -319.74747      39727.04      -315.02966      1.109151e+08 
     21000  -319.76264      39854.793     -315.02966      1.0990745e+08
     22000  -319.7997       40166.86      -315.02966      1.0446598e+08
     23000  -319.91061      41100.771     -315.02966      1.0605289e+08
     24000  -319.98762      41749.299     -315.02966      1.0312843e+08
     25000  -320.06842      42429.669     -315.02966      96790253     
     26000  -320.2321       43807.92      -315.02966      98941422     
     27000  -320.43008      45475.083     -315.02966      99172853     
     28000  -320.75368      48199.998     -315.02966      1.0304506e+08
     29000  -321.43727      53956.239     -315.02966      1.2359013e+08
     30000  -322.86003      65936.838     -315.02966      1.6426506e+08
     31000  -325.85698      91173.108     -315.02966      2.3460809e+08
     32000  -323.96663      75255.122     -315.02967      1.4386254e+08
     33000  -324.31173      78161.078     -315.02966      1.9611146e+08
     34000  -321.81048      57098.954     -315.02966      1.3183304e+08
     35000  -321.11553      51247.011     -315.02966      1.1860383e+08
     36000  -320.7006       47753.061     -315.02966      1.0988072e+08
     37000  -320.42875      45463.834     -315.02966      1.0486186e+08
     38000  -320.37522      45013.139     -315.02966      1.0667734e+08
     39000  -320.16625      43253.419     -315.02966      1.0141734e+08
     40000  -320.09034      42614.247     -315.02966      1.0082579e+08
     41000  -320.21558      43668.822     -315.02966      1.0548768e+08
     42000  -320.19431      43489.747     -315.02966      1.0242614e+08
     43000  -320.35932      44879.232     -315.02966      1.0646487e+08
     44000  -320.67457      47533.878     -315.02966      1.1366565e+08
     45000  -320.83512      48885.757     -315.02966      1.111537e+08 
     46000  -321.16647      51675.946     -315.02966      1.1302624e+08
     47000  -321.38122      53484.331     -315.02966      1.0507686e+08
     48000  -321.06774      50844.617     -315.02966      74672082     
     49000  -322.49756      62884.615     -315.02966      1.044115e+08 
     50000  -325.97731      92186.422     -315.02966      2.2498335e+08
     51000  -320.66106      47420.072     -315.02966      34605338     
     52000  -323.2278       69033.706     -315.02966      1.4817693e+08
     53000  -322.82489      65640.939     -315.02966      1.6065307e+08
     54000  -321.95574      58322.133     -315.02966      1.3860454e+08
     55000  -321.41375      53758.198     -315.02966      1.1831887e+08
     56000  -320.82121      48768.626     -315.02966      97374067     
     57000  -320.39876      45211.333     -315.02966      85881342     
     58000  -320.26394      44076.088     -315.02966      80873235     
     59000  -320.06828      42428.515     -315.02966      75885502     
     60000  -320.12912      42940.809     -315.02966      83005858     
     61000  -320.34086      44723.765     -315.02966      90748569     
     62000  -320.3942       45172.977     -315.02966      93992240     
     63000  -320.63122      47168.811     -315.02966      1.0726441e+08
     64000  -320.86235      49115.084     -315.02966      1.1515294e+08
     65000  -320.95075      49859.439     -315.02966      1.1705259e+08
     66000  -321.28995      52715.744     -315.02966      1.3144493e+08
     67000  -321.69035      56087.363     -315.02966      1.4188253e+08
     68000  -322.28755      61116.149     -315.02966      1.5220904e+08
     69000  -323.31574      69774.213     -315.02966      1.5914511e+08
     70000  -322.98352      66976.685     -315.02966      1.0382488e+08
     71000  -323.42006      70652.696     -315.02966      1.1257889e+08
     72000  -322.38839      61965.354     -315.02966      1.213394e+08 
     73000  -321.62733      55556.719     -315.02966      1.2062207e+08
     74000  -321.10333      51144.304     -315.02966      1.0628135e+08
     75000  -320.84916      49004.001     -315.02966      1.0188029e+08
     76000  -320.51651      46202.858     -315.02966      94118114     
     77000  -320.47427      45847.17      -315.02966      91437540     
     78000  -320.52773      46297.312     -315.02966      95165197     
     79000  -320.43972      45556.265     -315.02966      95366722     
     80000  -320.58645      46791.792     -315.02966      1.0182068e+08
     81000  -320.75509      48211.862     -315.02966      1.0907204e+08
     82000  -320.77091      48345.056     -315.02966      1.1257336e+08
     83000  -321.02219      50461.057     -315.02966      1.2376776e+08
     84000  -321.20064      51963.656     -315.02966      1.2909546e+08
     85000  -321.2856       52679.138     -315.02966      1.3104703e+08
     86000  -321.67229      55935.33      -315.02966      1.4072532e+08
     87000  -322.11917      59698.307     -315.02966      1.4404812e+08
     88000  -324.23523      77516.896     -315.02966      1.9731217e+08
     89000  -320.62579      47123.095     -315.02966      75893884     
     90000  -324.35107      78492.385     -315.02966      2.1044355e+08
     91000  -322.47803      62720.127     -315.02966      1.5538903e+08
     92000  -321.71623      56305.3       -315.02966      1.3227964e+08
     93000  -321.22259      52148.564     -315.02966      1.1511464e+08
     94000  -320.89326      49375.312     -315.02966      1.0320494e+08
     95000  -320.60652      46960.796     -315.02966      93163389     
     96000  -320.42504      45432.671     -315.02966      82638699     
     97000  -320.35025      44802.889     -315.02966      77728012     
     98000  -320.38016      45054.714     -315.02966      76753988     
     99000  -320.64823      47312.019     -315.02966      79089183     
    100000  -321.20665      52014.291     -315.02966      90654215     
    101000  -322.45176      62498.949     -315.02966      1.1671692e+08
    102000  -325.27551      86276.757     -315.02966      1.7450838e+08
    103000  -324.86597      82828.164     -315.02967      1.5358223e+08
    104000  -323.50288      71350.092     -315.02966      1.3914499e+08
    105000  -321.83206      57280.642     -315.02966      1.1374062e+08
    106000  -321.23029      52213.369     -315.02966      1.0154377e+08
    107000  -320.79552      48552.352     -315.02966      93581739     
    108000  -320.85374      49042.571     -315.02966      1.0230141e+08
    109000  -320.711        47840.638     -315.02966      98035102     
    110000  -320.92927      49678.547     -315.02966      1.0291687e+08
    111000  -321.37088      53397.184     -315.02966      1.161465e+08 
    112000  -321.64623      55715.825     -315.02966      1.2178973e+08
    113000  -323.29623      69609.916     -315.02966      1.5738912e+08
    114000  -326.43458      96036.881     -315.02966      2.2117147e+08
    115000  -326.29249      94840.366     -315.02967      2.1727072e+08
    116000  -323.49398      71275.138     -315.02966      1.6236371e+08
    117000  -321.69956      56164.918     -315.02966      1.2248665e+08
    118000  -321.03061      50531.902     -315.02966      1.114646e+08 
    119000  -320.58664      46793.421     -315.02966      1.0201646e+08
    120000  -320.31068      44469.633     -315.02966      92788900     
    121000  -320.33764      44696.673     -315.02966      96573809     
    122000  -320.29533      44340.406     -315.02966      96276795     
    123000  -320.48178      45910.447     -315.02966      96702563     
    124000  -320.99926      50267.91      -315.02966      1.1042709e+08
    125000  -321.72882      56411.316     -315.02966      1.2653574e+08
    126000  -323.76935      73593.887     -315.02966      1.6411768e+08
    127000  -323.84136      74200.288     -315.02967      1.2684596e+08
    128000  -325.27771      86295.322     -315.02966      1.7908195e+08
    129000  -322.44151      62412.6       -315.02966      1.2334056e+08
    130000  -321.33424      53088.672     -315.02966      1.0110915e+08
    131000  -320.74694      48143.276     -315.02966      87343006     
    132000  -320.58456      46775.879     -315.02966      84619630     
    133000  -320.42884      45464.64      -315.02966      80256772     
    134000  -320.41844      45377.068     -315.02966      79998095     
    135000  -320.67167      47509.417     -315.02966      88059739     
    136000  -320.94223      49787.695     -315.02966      94538899     
    137000  -321.61703      55469.964     -315.02966      1.1016475e+08
    138000  -323.12933      68204.503     -315.02966      1.4202379e+08
    139000  -326.08028      93053.485     -315.02966      1.894649e+08 
    140000  -326.22688      94287.865     -315.02967      1.9082785e+08
    141000  -323.43485      70777.215     -315.02966      1.4698731e+08
    142000  -321.79035      56929.435     -315.02966      1.1785802e+08
    143000  -321.17113      51715.2       -315.02966      1.0630317e+08
    144000  -320.72407      47950.681     -315.02966      94302254     
    145000  -320.53771      46381.4       -315.02966      89962864     
    146000  -320.57538      46698.572     -315.02966      90769921     
    147000  -320.65873      47400.459     -315.02966      88297290     
    148000  -321.05389      50727.942     -315.02966      95860956     
    149000  -321.86647      57570.413     -315.02966      1.1210695e+08
    150000  -323.71338      73122.627     -315.02966      1.4277977e+08
    151000  -325.52965      88416.746     -315.02967      1.7216009e+08
    152000  -325.82817      90930.57      -315.02966      1.8312663e+08
    153000  -322.5891       63655.44      -315.02966      1.2089115e+08
    154000  -321.32957      53049.334     -315.02966      96494848     
    155000  -320.66612      47462.65      -315.02966      81236441     
    156000  -320.47196      45827.713     -315.02966      78679995     
    157000  -320.33169      44646.581     -315.02966      75407967     
    158000  -320.42358      45420.371     -315.02966      76161171     
    159000  -320.79103      48514.483     -315.02966      84173108     
    160000  -321.27968      52629.281     -315.02966      92130817     
    161000  -322.50401      62938.95      -315.02966      1.138272e+08 
    162000  -325.40267      87347.575     -315.02966      1.6576028e+08
    163000  -323.59983      72166.432     -315.02967      1.1072655e+08
    164000  -324.04378      75904.823     -315.02966      1.4709858e+08
    165000  -322.01605      58829.972     -315.02966      1.0400742e+08
    166000  -321.15747      51600.213     -315.02966      82397014     
    167000  -320.8409       48934.422     -315.02966      73988066     
    168000  -320.58861      46810.029     -315.02966      64925698     
    169000  -320.54312      46426.959     -315.02966      61942158     
    170000  -320.68604      47630.438     -315.02966      64309567     
    171000  -320.77008      48338.134     -315.02966      63324927     
    172000  -321.08474      50987.727     -315.02966      69721832     
    173000  -321.6134       55439.431     -315.02966      80485473     
    174000  -322.41904      62223.44      -315.02966      94329801     
    175000  -324.95819      83604.705     -315.02966      1.5681125e+08
    176000  -321.71907      56329.278     -315.02966      45217519     
    177000  -324.24577      77605.673     -315.02966      1.5164385e+08
    178000  -322.34082      61564.766     -315.02966      1.0677988e+08
    179000  -321.3229       52993.228     -315.02966      80528491     
    180000  -320.91614      49567.992     -315.02966      70928167     
    181000  -320.79771      48570.793     -315.02966      70105356     
    182000  -320.43289      45498.72      -315.02966      62263793     
    183000  -320.59821      46890.81      -315.02966      67986358     
    184000  -320.64879      47316.739     -315.02966      70175355     
    185000  -320.52287      46256.459     -315.02966      68704646     
    186000  -320.94252      49790.187     -315.02966      81368769     
    187000  -321.10174      51130.914     -315.02966      84251825     
    188000  -321.38014      53475.167     -315.02966      91376642     
    189000  -322.14722      59934.547     -315.02966      1.1198813e+08
    190000  -322.9004       66276.794     -315.02966      1.2823518e+08
    191000  -323.63455      72458.807     -315.02966      1.6144592e+08
    192000  -324.3348       78355.338     -315.02966      1.5544396e+08
    193000  -321.63344      55608.185     -315.02966      85813641     
    194000  -323.54261      71684.651     -315.02966      1.4340251e+08
    195000  -323.1577       68443.449     -315.02966      1.5089288e+08
    196000  -322.90055      66278.083     -315.02966      1.4392954e+08
    197000  -322.45751      62547.374     -315.02966      1.2607137e+08
    198000  -322.18257      60232.201     -315.02966      1.137101e+08 
    199000  -322.24297      60740.76      -315.02966      1.0950975e+08
    200000  -322.47749      62715.575     -315.02966      1.070732e+08 
    200571  -323.24897      69211.97      -315.02966      1.1694375e+08
Loop time of 86.0986 on 1 procs for 200000 steps with 101 atoms

Performance: 20070.020 fs/day, 0.001 hours/fs, 2322.919 timesteps/s, 234.615 katom-step/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 85.691     | 85.691     | 85.691     |   0.0 | 99.53
Neigh   | 0.0010104  | 0.0010104  | 0.0010104  |   0.0 |  0.00
Comm    | 0.016762   | 0.016762   | 0.016762   |   0.0 |  0.02
Output  | 0.061098   | 0.061098   | 0.061098   |   0.0 |  0.07
Modify  | 0.22948    | 0.22948    | 0.22948    |   0.0 |  0.27
Other   |            | 0.09905    |            |       |  0.12

Nlocal:            101 ave         101 max         101 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:              0 ave           0 max           0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:           5050 ave        5050 max        5050 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 5050
Ave neighs/atom = 50
Neighbor list builds = 46
Dangerous builds = 0

unfix		1
undump		1
undump		2

Total wall time: 0:01:28
